Yes you will have two extra wires on your bike. On a stock bike there are three tail light wire, hot at all time, brake and ground. Each turn signal has two wires, power and ground. Your new tail light has five wires, one hot at all time, one brake light, one left turn signal, one right turn signal and one ground. When installing new light the two ground wires for the turn signal won't be used, just leave them tied up under your seat. You will just use the one ground wire for the tail light. Because it's a complete assembly they share the one ground. As for the actual connectors being different, it's up to you how you connect them. I just mickey moused them together, or you can solder them.
Here a link to some instructions to the tail light I installed, it might help illustrate things. Keep in mind there diagram of the bike harness does not show the ground wires for the turn signals.
Instructionsgood luck!